Like phosphorylation, protein ubiquitination is a reversible process to regulate essentially all cellular events. Misregulation of ubiquitination plays an important role in the pathogenesis of a variety of diseases, ranging from cancer to neurodegenerative disorders. Although some proteomics tools have been developed to analyze ubiquitinated proteins in yeast, it is still difficult to perform similar analysis in mammalian cells. The goal of this application is to develop a series of proteomics tools to analyze ubiquitinated proteome including: (i) to establish a method of tandem affinity purification to purify Ub-conjugates in mammalian cells;(ii) to develop a strategy to enrich subsets of ubiquitinated proteins that are modified by specific polyUb linkages;(iii) to develop proteomic methods to profile Ub-conjugates and to evaluate false positives. These quantitative mass spectrometry strategies will be implemented to investigate the dynamics of ubiquitinated proteome under different conditions. Taken together, the studies will invent essential tools for exploring ubiquitinated proteome and a better understanding of heterogeneity of polyUb chain structures, which plays an important role in ubiquitin signaling and disease development. PUBLIC HEALTH RELEVANCE: Like phosphorylation, protein ubiquitination is a reversible process to regulate essentially all cellular events. Misregulation of ubiquitination plays an important role in the pathogenesis of a variety of diseases, ranging from cancer to neurodegenerative disorders. The goal of this application is to develop novel proteomics technologies to analyze protein substrates that are modified by specific ubiquitin polymers. Once established, the technologies will enable investigation of the specificity of ubiquitin signaling and its involvement in ubiquitin- related diseases.